Science: meet the microbes with altitude

Air samples taken up to 15km above the earth’s surface have revealed a rich variety of microbial life

As microbiologists are discovering, Earth is populated with umpteen trillions of bacteria from the top of the atmosphere to rocks deep underground, from the human gut to superheated ocean vents. The upper atmosphere is the latest of these “microbiomes”, as the microbial communities are known, to go under the scientific spotlight.

A team at the Georgia Institute of Technology in Atlanta analysed air samples taken from the middle and upper troposphere 8km-15km above the earth’s surface. The researchers discovered a surprisingly high density and variety of microbes. “We did not expect to find so many micro-organisms in the troposphere, which is considered a difficult environment for life,” says Kostas Konstantinidis of Georgia Tech. “There seems to be quite a diversity of species.”

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The samples were taken during a mission by the US space agency Nasa to study atmospheric conditions associated with tropical storms. A DC8 aircraft, flying over the Caribbean, Atlantic and nearby landmasses during the 2010 hurricane season, captured microscopic particles on air filters. Genomic techniques were used for the microbiological analysis – detecting microbes and estimating their quantities from their DNA, rather than using conventional cell culture techniques.

The results, published in Proceedings of the National Academy of Sciences, showed that viable bacterial cells represented around 20 per cent of all particles detected in the submicron size range. Fungi were present too but much less common than bacteria.

The microbes are blown into the troposphere through the same atmospheric processes that sweep up dust and salt particles. So it is not surprising the sampling found mainly marine bacteria in air masses that originated over the ocean and terrestrial bacteria in air that originated over land. Nor is it surprising that hurricanes Earl and Karl, with their ferocious updrafts, raised the microbial population in the troposphere.

Seventeen different bacteria “taxa” (types) were present in all samples, including some that can metabolise carbon compounds that are ubiquitous in the atmosphere, such as oxalic acid. This raises the possibility that microbes may inhabit the troposphere on a more permanent basis, growing and reproducing there.

Microbes are likely to play a role in the weather. “In the absence of dust or other materials that could provide a good nucleus for ice formation, just having a small number of these micro-organisms around could facilitate the formation of ice at these altitudes and attract surrounding moisture,” says Athanasios Nenes of Georgia Tech. “If they are the right size for forming ice, they could affect the clouds around them.”

Double trouble: the duplicate grant problem

Investigators using text-matching technology have uncovered a new, or previously unremarked, source of scientific misconduct: receiving grants from more than one funding agency for the same project.

Under pressure

Researchers sponsored by the European Space Agency have developed a way to measure the pressure inside the skull for head injury or brain surgery patients, using headphone sound waves.

Harold Garner and colleagues at the Virginia Polytechnic Institute say agencies unwittingly have spent millions of dollars on undeclared duplicate grants. Their analysis, published in Nature, is based on a comparison of 858,000 grant and contract summaries from five US funding bodies, using text similarity software devised originally to spot plagiarism in scientific papers. This was supplemented by manual review of suspect cases.

The researchers could not tell definitively which similar projects were true duplicates, without access to the full grant files, which are not publicly available. But they found strong evidence that tens of millions of dollars were spent on grants where at least part of the work was already funded.

“It is quite possible our software missed many cases of duplication,” Garner says. “If text similarity software misses as many cases of funding duplications as it does plagiarism of scientific papers we’ve studied, the extent of duplication could be much larger – as much as 2.5 per cent of research funding, equivalent to $5.1bn since 1985.”

Modern word-processing technology makes it easy for researchers – keen to win funding in an increasingly competitive environment – to submit multiple proposals to different agencies, by copying and pasting text and diagrams between applications. The wording may be adjusted slightly but describes essentially the same project.

At the same time, however, text mining makes it easier to detect multiple applications, as the Virginia Tech authors did. Supported by a Nature editorial, they urge the world’s research funding bodies to set up online databases of grants and use them to ensure they are not duplicating one another’s work.

Japanese scientists have filmed the remarkable underwater hunting techniques of Adélie penguins in Antarctica, writes Ling Ge. Researchers at the National Institute of Polar Research in Tokyo wanted to understand exactly how penguins hunt. “It is now possible to examine what, where, when and how marine animals catch prey in the water,” says Yuuki Watanabe, lead author.

Previous studies have achieved direct recordings from video cameras attached to marine animals only for short periods. Indirect signals (such as stomach temperature) recorded by sensors attached to penguins have not been validated in the field.

“We effectively extended the recording periods of a small video camera by linking visual inspection to indirect signals,” says Watanabe. The team took an integrated approach, attaching tiny video cameras and accelerometers to the heads and backs of 14 free-swimming Adélie penguins in Lützow-Holm Bay. The videos, which lasted about 15 hours in total, show penguins feeding on their favourite food: shrimp-like krill and fish called bald notothens.

The birds are masterly hunters: fast and efficient. They can catch as many as two krill per second, and on average consume around 200 krill and 30 fish per hour.

The scientists found that the birds have different strategies and success rates depending on whether the prey is krill or fish. Krill were captured at a range of depths, while fish were caught only at shallow depths underneath the sea ice.

The study is published in Proceedings of the National Academy of Sciences.

3D printing’s new celling point

Human embryonic stem cells (hESCs) are the latest material for 3D printing. A new technique developed in Scotland could be used first to speed up drug testing and later to create new tissues and organs for transplantation.

“To the best of our knowledge, this is the first time that hESCs have been printed,” says Will Wenmiao Shu of Heriot-Watt University. “The generation of 3D structures from hESCs will allow us to create more accurate human tissue models, which are essential for in vitro drug development and toxicity testing.”

The Heriot-Watt researchers, working with Roslin Cellab, a local biotechnology company, designed a gentle valve-based technique adapted to the delicate nature of hESCs. The printing is controlled by varying pneumatic pressure and opening and closing a microscopic nozzle.

The stem cells were printed from two separate reservoirs on to a plate in a preprogrammed pattern. The researchers confirmed not only that the concentration and distribution of hESCs was right but also that the cells remained alive and “pluripotent” – able to differentiate into any other cell type.

“In the longer term, we envisage the technology being further developed to create viable 3D organs for medical implantation from a patient’s own cells, eliminating the need for organ donation, immune suppression and the problem of transplant rejection,” says Shu.